pymol-users

Hi again, list.
I need help on how to render an unconventional (non-protein) pdb file with a big number of atoms in it. Even with no display (console mode), pymol still crashes due to insufficient memory.
A different hardware is out of the question and a smaller file would defeat my purpose, so I would like to simplify the representation. What i do is to 'show sphere', then 'set sphere_scale,0.01'. However, it seems it takes the same amount of memory for pymol to display small or large spheres (i thought that by using very small sphere_scale, pymol would tend to treat each atom more and more as a single pixel). The dots representation is also very complex to display I believe. In my case the line display can not be used either.
Are there some settings to increase the memory allocated to pymol ?
Are there settings of the dots representation so that only one dot is represented for each atom ?
Any additional ideas are of course welcome !
Thanks in advance !
Garteiser Philippe
OMRF, Cardiovascular Biology dpt.
Doctoral candidate, OU Bioengineering
Advisors: Dr. Tim Mather, Dr M. Uli Nollert
12600 N Macarthur
Crown Pointe apt. #1423
Oklahoma City, OK 73142
home: (405) 603 7091
work: (405) 271 4924
"It does not pay to leave a live
dragon out of your calculations"
- Tolkien

Hi Philippe,
Pymol isn't very good at handling many spheres. However, Povray is
extremely efficient with raytracing scenes consisting of spheres and
if you know the perspective you want to have the image from, you can
convert your atom set to spheres (with desired radii) and apply the
view from Pymol. If you would like, I can send you the script (Povray
macro) to export the Pymol view to Povray.
Best regards,
Tsjerk
On 7/25/06, Philippe.Garteiser-1@... <Philippe.Garteiser-1@...> wrote:
> Hi again, list.
>
> I need help on how to render an unconventional (non-protein) pdb file with a big number of atoms in it. Even with no display (console mode), pymol still crashes due to insufficient memory.
> A different hardware is out of the question and a smaller file would defeat my purpose, so I would like to simplify the representation. What i do is to 'show sphere', then 'set sphere_scale,0.01'. However, it seems it takes the same amount of memory for pymol to display small or large spheres (i thought that by using very small sphere_scale, pymol would tend to treat each atom more and more as a single pixel). The dots representation is also very complex to display I believe. In my case the line display can not be used either.
>
> Are there some settings to increase the memory allocated to pymol ?
> Are there settings of the dots representation so that only one dot is represented for each atom ?
> Any additional ideas are of course welcome !
>
> Thanks in advance !
>
> Garteiser Philippe
> OMRF, Cardiovascular Biology dpt.
> Doctoral candidate, OU Bioengineering
> Advisors: Dr. Tim Mather, Dr M. Uli Nollert
> 12600 N Macarthur
> Crown Pointe apt. #1423
> Oklahoma City, OK 73142
> home: (405) 603 7091
> work: (405) 271 4924
>
> "It does not pay to leave a live
> dragon out of your calculations"
> - Tolkien
>
>
>
>
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--
Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336

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